visualiseQualityParameters    package:arrayMagic    R Documentation

_G_r_a_p_h_i_c_a_l _r_e_p_r_e_s_e_n_t_a_t_i_o_n _o_f _q_u_a_l_i_t_y _p_a_r_a_m_e_t_e_r_s

_D_e_s_c_r_i_p_t_i_o_n:

     Graphical representation of quality parameters

_U_s_a_g_e:

     visualiseQualityParameters(qualityParameters, savePath, fileName="visualiseQualityParametersOutput.pdf", width=25, height=25, plotOutput="pdf")

_A_r_g_u_m_e_n_t_s:

qualityParameters: 'data.frame'; required;  contained in the return
          value of 'qualityParameters' 

fileName: character string; required; default:
          "visualiseQualityParametersOutput.pdf" 

savePath: character string; optional; default: missing

   width: graphics window width

  height: graphics window height

plotOutput: character string; required; either "screen", "pdf" or
          "win.metafile"; default: "pdf"

_D_e_t_a_i_l_s:

     For details on the specific parameters see 'qualityParameters'.
     Lines are only used for easier detection of outliers. The ordering
     of the hybridisation is somehow arbitrary, and only reflects the
     (initial) ordering.  The "correlation" line for example
     graphically represents the correlation coefficients calculated
     between the green and red channel for each hybridisation. The
     horizontal blue line is drawn at the height of one. The function
     'qualityDiagnostics' calls 'visualiseQualityParameters'.

_V_a_l_u_e:

     A graphical representation of quality parameters.
     'qualityDiagnostics' does call 'visualiseQualityParameters'

_A_u_t_h_o_r(_s):

     Andreas Buness <a.buness@dkfz.de>

_S_e_e _A_l_s_o:

     'qualityParameters'; 'qualityDiagnostics'

_E_x_a_m_p_l_e_s:

             

